visualiseQualityParameters    package:arrayMagic    R Documentation

_G_r_a_p_h_i_c_a_l _r_e_p_r_e_s_e_n_t_a_t_i_o_n _o_f _q_u_a_l_i_t_y _p_a_r_a_m_e_t_e_r_s

_D_e_s_c_r_i_p_t_i_o_n:

     Graphical representation of quality parameters

_U_s_a_g_e:

     visualiseQualityParameters(qualityParameters, savePath, fileName="visualiseQualityParametersOutput.pdf", width=25, height=25, plotOutput="pdf")

_A_r_g_u_m_e_n_t_s:

qualityParameters: 'data.frame'; required;  contained in the return
          value of 'qualityParameters' 

fileName: character string; required; default:
          "visualiseQualityParametersOutput.pdf" 

savePath: character string; optional; default: missing

   width: graphics window width

  height: graphics window height

plotOutput: character string; required; either "screen", "pdf" or
          "win.metafile"; default: "pdf"

_D_e_t_a_i_l_s:

     For details on the specific parameters see 'qualityParameters'.
     Lines are only used for easier detection of outliers. The ordering
     of the hybridisation is somehow arbitrary, and only reflects the
     (initial) ordering.  The "correlation" line for example
     graphically represents the correlation coefficients calculated
     between the green and red channel for each hybridisation. The
     horizontal blue line is drawn at the height of one. The function
     'qualityDiagnostics' calls 'visualiseQualityParameters'.

_V_a_l_u_e:

     A graphical representation of quality parameters.
     'qualityDiagnostics' does call 'visualiseQualityParameters'

_A_u_t_h_o_r(_s):

     Andreas Buness <a.buness@dkfz.de>

_S_e_e _A_l_s_o:

     'qualityParameters'; 'qualityDiagnostics'

_E_x_a_m_p_l_e_s:

             

